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Several biotech companies use lipid nanoparticles (top) to shuttle mRNA (orange-yellow) into cells, where the ribosome (bottom right) translates it into therapeutic proteins (bottom left).

On a brisk morning in April, dozens of investors filed into a Marriott hotel conference hall in Kendall Square, the biotech hub of Cambridge, Mass., for the first Moderna Therapeutics platform science day. They gathered hoping to get a rare, inside look at the science behind what the start-up had long claimed to be a disruptive drug platform: carefully designed molecules called messenger RNA that prompt the body to make its own medicine. The concept has attracted billions in funding, but the company had largely kept details of how the technique works under wraps.

In brief

Used by all living things to make proteins, messenger RNA is one of the least explored frontiers of drug discovery. Moderna Therapeutics, and an increasing number of similarly well-funded biotech firms, is built on the promise that mRNA can be turned into a powerful treatment for genetic diseases, cancer, infectious diseases, and more. But turning mRNA into a drug is far from trivial, and companies have kept their technology largely under wraps. Now, Moderna is offering a glimpse of its massive research engine. Read on to learn how researchers are trying to move mRNA out of the lab and into the clinic.﻿

“Why are we so passionate about messenger RNA?” Moderna President Stephen Hoge asked the attentive audience. “It starts with the question of life,” he explained. “And in fact, all life that we know flows through messenger RNA. ... In our language, mRNA is the software of life.”

Cells use mRNA to translate the static genes of DNA into dynamic proteins, involved in every bodily function, Hoge explained. Biotech companies make some of these proteins as drugs in large vats of genetically engineered cells. It’s a time-consuming and costly process.

Moderna offered a different proposition: What if instead, mRNA was given therapeutically? In theory, it could prompt proteins to be made in your body. It would put the drug factory inside you.

The idea Hoge was selling is straightforward, but its implementation is not. When mRNA is injected into the body, it triggers virus-detecting immune sensors. That event causes cells to shut down protein production, thus foiling the therapy. And even if the molecule makes it into the cell—another challenge that has long vexed drug delivery experts—the mRNA might not make enough protein to actually be useful.

Moderna now employs more than 600 people, the majority of them scientists, and spends enormous sums—over $450 million in the past five years—learning how to make and improve its mRNA therapies. This year, the firm will invest another $100 million. It’s an astonishing sum for a company that is still years away from a marketed product or even a late-stage experimental drug. Hoge told investors at the R&D day that his firm has no intention of slowing the pace of its investment. “Over the next five years we will invest the next half billion dollars.”

Indeed, just a few months later, Moderna executives were making their next splashy move: opening the doors to their first drug manufacturing plant, in Norwood, Mass. The $110 million project gives Moderna full control over the mRNA used in its preclinical and clinical studies.

Credit: Moderna Therapeutics

Moderna Therapeutics President Stephen Hoge and Chief Scientific Officer Melissa Moore at the firm's headquarters. Moore has played a key role in making some of the company's science public.

It’s all part of CEO Stéphane Bancel’s long-term vision to transform the drug industry the same way that the first biotech companies, like Amgen, Biogen, and Genentech, did when they began developing protein therapies called biologics in the eighties. Biologics are now the fastest-growing segment of the drug industry, and in theory, mRNA could replace them all. “This is a 20-year job,” Bancel told the R&D day crowd. “We believe we are just starting.”

Moderna’s slick storytelling has helped Bancel raise over $1.7 billion—all from private investors—to try to realize his ambitious plan. It has also invited skeptics, who would like to see those ambitions backed up by data.

But Moderna has catalyzed an excitement for therapeutic mRNA that is spilling into other start-ups and even big pharma companies. Collectively, they think they have overcome some of the fundamental challenges of translating mRNA from idea to product. Years of behind-the-scenes research have created a surprisingly deep, but early-stage, pipeline of mRNA therapeutics. Already, mRNA is being tested in a dizzying array of studies, including therapies for rare genetic diseases, cancer immunotherapies, and vaccines for infectious diseases.

“You could ultimately use mRNA to express any protein and perhaps treat almost any disease,” Hoge said in a recent interview with C&EN. “It is almost limitless what it can do.”

Birth of a disrupter

Although Moderna helped put mRNA therapeutics on the map, efforts to use it as a therapy predate the company by at least two decades. In 1990, University of Pennsylvania scientist Katalin Karikó proposed using mRNA as an alternative to DNA-based gene therapy. Both techniques can produce therapeutic proteins, but while DNA’s effect is permanent, mRNA offers a temporary fix. Karikó reasoned that would alleviate some of the long-term safety concerns surrounding gene therapy, “but nobody was interested,” she says.

At the time, mRNA was difficult to work with. Scientists could isolate only small amounts of the material, which was then easily destroyed by RNA-chopping enzymes found on skin and in the air. And immune reactions to mRNA injections in animals suggested the technique wasn’t as safe as Karikó had hoped.

You could ultimately use mRNA to express any protein and perhaps treat almost any disease.

Stephen Hoge, president, Moderna Therapeutics

She forged ahead anyway and, with her colleague Drew Weissman, made a simple but game-changing discovery in 2005. The researchers replaced one of mRNA’s four chemical building blocks, a nucleoside called uridine, with a slightly modified nucleoside called pseudouridine. Amazingly, the modified mRNA evaded immune sensors (Immunity 2005, DOI: 10.1016/j.immuni.2005.06.008). “We submitted that for a patent, and that was the birth of therapeutic RNA,” Weissman says.

In 2006, Karikó started her own mRNA therapy company. Her start-up quickly dissolved, but three German firms—CureVac, BioNTech, and Ethris—would soon have more success. Ingmar Hoerr, cofounder of CureVac, won the first major funding for the field that year. “mRNA is like a memory stick,” Hoerr recalls explaining to software billionaire Dietmar Hopp. “You can just plug the memory stick into the body, it reads the information, makes any protein you want, and the body cures itself.” Hopp led a $26 million investment in the company.

Although the field was still largely under the radar, other labs began copying Karikó and Weissman’s trick. In 2010 Harvard University scientist Derrick Rossi used modified mRNA to encode proteins that reprogrammed adult cells into embryonic-like stem cells. Harvard cardiovascular scientist Kenneth Chien, now at the Karolinska Institute, and Massachusetts Institute of Technology’s famed serial entrepreneur Robert Langer spotted mRNA’s therapeutic potential and joined Rossi in pitching a stem cell company to the venture capital firm Flagship Pioneering.

Flagship’s CEO, Noubar Afeyan, saw a much farther flung potential for mRNA. He asked the group to explore mRNA as a tool for making all kinds of protein therapies. The academics subsequently showed that modified mRNA injected into mice could produce proteins in the liver that were secreted and circulated in the blood. Afeyan was sold. The quartet founded Moderna in 2010, and Afeyan recruited Bancel as CEO the next year.

After spending two years in stealth mode, Moderna burst onto the biotech scene in 2012 with $40 million from Flagship and other investors. It wouldn’t take long for more money to pile up.

In their academic labs, Rossi and Chien injected mRNA encoding a protein called vascular endothelial growth factor (VEGF) directly into the hearts of mice. Scientists had long surmised that VEGF could heal heart tissue damaged during a heart attack, but VEGF proteins don’t stick around long enough, so simply injecting the proteins doesn’t work. The VEGF-encoding mRNA, however, lingered in cells, making enough of the protein to improve the animals’ survival and health after a heart attack (Nat. Biotechnol. 2013, DOI: 10.1038/nbt.2682).

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That study formed the backbone of Moderna’s first big pharma partnership, a collaboration with AstraZeneca in 2013 that included a $240 million investment. After replicating the VEGF experiment in mice and pigs, AstraZeneca launched a study to test the therapy in people who recently had heart attacks. It’s now Moderna’s most advanced program, in a Phase II clinical trial.

Since then, Moderna has struck additional pharma partnerships and earned itself a reported valuation of more than $7 billion. “Moderna was so important because they brought attention to the field,” Hoerr says. Subsequent to Moderna’s AstraZeneca partnership, CureVac raised more than a $100 million and forged partnerships with Boehringer Ingelheim and Eli Lilly & Co. to develop mRNA therapies for cancer.

BioNTech, founded in 2008, has also undergone a recent growth spurt. In the past three years it has inked mRNA drug development deals with Sanofi, Genentech, and Pfizer, and earlier this year it raised $270 million in private funds. “It took a while for the pharmaceutical community to really get their head around the mRNA approach,” Sean Marett, BioNTech’s chief business officer, says. “Now all pharmaceutical companies are looking at mRNA.”

mRNA is the software of life.

Stephen Hoge, president, Moderna Therapeutics﻿

As investors lined up for mRNA companies, so did the critics. Moderna hasn’t released any data from the VEGF trial yet, and until 2017, Rossi and Chien’s study was the only scientific research publication that the company could point to as validation of its technology.

Moderna kept its science under the radar by continuing to raise funds from private investors rather than become a publicly traded company. That decision, coupled with its executives’ propensity to aggrandize its mission, has instilled a reputation of secrecy—and a skepticism around its technology—that has proved hard to shake. It doesn’t help that there are only a handful of academic scientists working in the largely industry-dominated mRNA therapy field. “I would much rather know what is going on in the field and be able to learn from everyone else,” Weissman says. “Right now they are all learning from us.”

And as cash continues to flow into the field, expectations continue to rise. “There is huge momentum now,” Hoerr says. “And since everybody is promising something, everybody has to deliver.”

Credit: Michelle Lynn Hall/Moderna Therapeutics

Michelle Lynn Hall, a computational chemist at Moderna, studies how mRNA (ball-and-stick model) interacts with various proteins, such as decapping enzymes (gray) that destabilize the molecule. Models like the one shown here can help scientists optimize their mRNA.

Moderna unveiled

For any of these firms to be successful, they need to prove themselves capable of solving a few key problems: avoiding an immune reaction, safely shuttling the therapy into the appropriate cells, and making sure the mRNA yields enough protein to have an effect. On that April morning in Kendall Square, Moderna began to pull back the curtain on its efforts to overcome these challenges.

Melissa Moore, who was brought on as chief scientific officer in late 2016, has been at the center of this movement toward transparency. Moore brings a distinguished pedigree to the start-up. She was a postdoc in geneticist Phillip Sharp’s lab at MIT when he won the Nobel Prize in Physiology or Medicine in 1993 for his work on RNA. Moore then went on to study RNA as a Howard Hughes Medical Institute investigator for nearly two decades and was a founding codirector of the RNA Therapeutics Institute at the University of Massachusetts Medical School.

Anatomy of an mRNA

Scientists are learning how to modify and control mRNA to make it more druglike for predictable protein production.

5' cap: The endcap offers a foothold to initiate the process of translating the mRNA into a protein. Decapping enzymes also bind here to break down mRNA. In humans, the cap is normally a molecule called 7-methylguanosine linked to the mRNA via a triphosphate bridge, but chemists are creating new caps to maximize protein translation and ward off decapping enzymes.

5' UTR: This untranslated region is key for determining how efficiently the mRNA is translated into a protein. It can also affect the mRNA’s stability.

Coding region: The ribosome, the cell’s protein-making machinery, reads this sequence and translates it to produce a protein. Because there are many different ways to write an mRNA code that will lead to the creation of the same protein, scientists look for variants that produce their desired amount of protein.

3' UTR: Modifying this untranslated region can increase or decrease the mRNA’s stability. Scientists can also add a code here called a microRNA target sequence that limits which cells use the mRNA.

Poly(A) tail: A long sequence of adenosines (A), usually more than 100 of them, protects this end of the mRNA from degradation.

Whole mRNA: Using modified nucleosides, such as pseudouridine in place of the normal uridine, helps the mRNA evade immune cell and intracellular sensors that detect foreign RNA. Changing the sequence also alters how the lengthy mRNA strand interacts with itself, a way of controlling the speed of protein production.

Under Moore’s watch, Moderna’s scientific shyness has begun to abate. The company published a dozen mRNA research studies in 2017, and several more are on the way. “We are discovering things that we hope will rewrite the textbooks,” she says.

Those discoveries involve deciphering the molecular rules for changing the potency and longevity of mRNA molecules. The doses of traditional drugs are carefully measured before they are used, but the amount of protein that a single mRNA makes can vary widely. Cells can reuse a single mRNA to make on the order of 1,000 to 10,000 proteins. Controlling that number will help mRNA work more like traditional therapies.

One way to tune the amount of protein an mRNA makes is called codon optimization. There are many ways to write an mRNA code to produce the exact same protein, and the possible number of variants is often too large to test experimentally. So Moderna data scientist Andrew Giessel is using machine learning to determine the rules for changing an mRNA sequence to produce more or less protein, as desired. Moore says a publication describing his methods is in the works.

Actually getting the mRNA into cells is another challenge. A common solution is to wrap the mRNA in fatty vessels called lipid nanoparticles. Scientists have labored for years to make these vessels safe and effective while developing another kind of therapy, called small interfering RNA (siRNA). Chemists eventually ironed the kinks out for delivering siRNA, but those molecules are only 20 or so nucleotides long. mRNAs, meanwhile, span hundreds to thousands of nucleotides and will thus require newly designed lipid nanoparticles.

The importance of delivery is not lost on Moderna. It’s the area with the most room for improvement and the biggest focus for the company’s chemists, Moore says. One proxy for success is how much mRNA escapes from endosomes, the cellular structures that ingest lipid nanoparticles. Moore says Moderna’s current favorite lipid nanoparticle, N1GL, breaks out of the endosome 25 times as much as standard lipid nanoparticles (Mol. Ther. 2018, DOI: 10.1016/j.ymthe.2018.03.010).

An even bigger long-term challenge will be getting mRNA into specific cells of the body. Lipid nanoparticles have a tendency to aggregate in the liver. That could make mRNA useful for producing therapeutic proteins and antibodies that are secreted from liver cells and circulated in the bloodstream. But getting mRNA therapies into other organs will require either direct injection into that tissue—as in AstraZeneca’s post-heart attack VEGF study—or fancy new control systems.

Moderna has revealed the blueprints for one such system used to ensure its mRNA is made only inside cancer cells. Moderna scientist Ruchi Jain designed an mRNA that causes cancer cells to self-destruct but is recognized by, and destroyed in, healthy cells (Nucleic Acid Ther. 2018, DOI: 10.1089/nat.2018.0734).

Moderna isn’t divulging all its secrets. But even these glimpses of its research engine suggest it has scientists devoted to nearly every conceivable aspect of turning mRNA into a therapy. “There is no reason to believe it can’t be done,” Hoge told the investor crowd in April. “There is every reason to believe it is going to be hard.”

mRNA’s many applications

If Moderna and others can work out all the technical challenges, mRNA’s killer application could be making protein therapies inside cells, a place that biologic drugs cannot go. Many rare genetic diseases are marked by dysfunctional or deficient proteins.

The most advanced program in the field got its start in 2008, when Shire Pharmaceuticals quietly began working on mRNA therapies for people with cystic fibrosis. The goal was to replace the broken CFTR proteins, found in the lungs of people with the disease, with fully functional CFTR copies.

Led by Michael Heartlein, in 2011 the Shire team began collaborating with a new German mRNA start-up called Ethris to develop a cystic fibrosis mRNA therapy with lipid nanoparticles that could hold up under the pressure of being aerosolized for inhalable delivery into the lungs. “It was not an easy task,” Heartlein says. “Lots of work, lots of trial and error, and lots of formulations that didn’t pan out or weren’t safe.”

Shire sold its mRNA programs to a start-up called RaNA Therapeutics in 2017, and Heartlein left to become CSO of the firm. RaNA later rebranded itself as Translate Bio, and this June it became the first publicly traded mRNA start-up, raising $122 million in its initial public offering.

Another company, Vertex Pharmaceuticals, has already received U.S. Food & Drug Administation approval for multiple small-molecule drugs that improve lung function in many people with cystic fibrosis. Still, the possibility of making a fully functional, correct version of CFTR with mRNA has allure. Vertex’s drugs are not effective across all the mutations that cause the disease, but a single mRNA therapy could treat everyone. Translate Bio’s cystic fibrosis mRNA therapy is now in a Phase I clinical study, making it the first company to test an mRNA therapy for a rare genetic disease in humans. Moderna and Vertex Pharmaceuticals are working on a similar treatment, still in preclinical stages.

But most of the money in the mRNA field has gone to a different application of the technology: vaccines. Traditional vaccines use bits of injected proteins to train the immune system to take down future viruses displaying those same proteins. Manufacturing them takes months, a timescale too slow to combat emerging epidemics. mRNA vaccines, on the other hand, simply encode these protein fragments in a single mRNA strand. And as mRNA companies optimize and scale up their enzymatic production of mRNA, scientists anticipate these vaccines could be made in a matter of weeks.

It’s considered the easiest test case of the technology, since the mRNA needs to produce only a small amount of protein for the vaccine to work, and setting off the body’s RNA immune sensors a little won’t hurt. “It is low-hanging fruit,” Weissman says.

Its potential has still spurred several major mRNA vaccine collaborations: The U.S. government and the Bill & Melinda Gates Foundation invested in Moderna’s mRNA vaccine programs for diseases caused by viruses like Zika and HIV; Sanofi partnered with Translate Bio to develop infectious disease mRNA vaccines; and Pfizer last month teamed up with BioNTech to develop mRNA flu vaccines.

Many companies think mRNA vaccines can help the immune system tackle cancer too. There are many variations of the technique, but in general the mRNA encodes proteins made on cancer cells, which teaches the immune system to recognize and target tumors. CureVac is developing mRNA cancer vaccines alone and in partnerships with Boehringer Ingelheim and Eli Lilly & Co. BioNTech has multiple programs of its own too. And Merck & Co. made a splash into the field through a $200 million deal with Moderna in 2016 and another $125 million this year.

Moderna and Merck are taking the technology a step further to develop individualized cancer vaccines, in which a unique therapy is designed and manufactured for each patient. It starts with a tumor biopsy, genetic sequencing, and a proprietary algorithm that picks 20 tumor mutations that are most likely to help the immune system home in on the cancer. Those mutations are encoded into an mRNA, which is injected into the patient’s muscle and used to provide a molecular mug shot that sends the immune system seeking tumors. Genentech and BioNTech have a similar program, and results from the first 13 people stoked excitement for the technology (Nature 2017, DOI: 10.1038/nature23003), but larger studies will be required to prove its worth.

Plowing ahead

Moderna, along with the mRNA field at large, still has a lot to prove. So far, it has published human data only from its early-stage flu vaccine study (Mol. Ther. 2017, DOI: 10.1016/j.ymthe.2017.03.035). Bigger studies lie ahead, and Moderna is wasting no time on its trek toward becoming the next major biotech.

Credit: Moderna Therapeutics

Moderna's new manufacturing facility, which opened in Norwood, Mass., in July, is supplying mRNA for the company's clinical trials.

In a forested pocket of Norwood, Mass., a 45-minute drive south of Kendall Square, Moderna’s glistening new drug factory is hard at work making mRNA. Upstairs, an army of machines and robotic handlers, accompanied by a few scattered employees, are each month creating up to 1,000 batches of new mRNA molecules for preclinical testing.

Downstairs, in a series of clean rooms, enzymes repetitively transcribe DNA templates into copious strands of mRNA, which are then formulated into lipid nanoparticles for the company’s expansive clinical pipeline.

Since everybody is promising something, everybody has to deliver.

Ingmar Hoerr, cofounder, CureVac﻿

Human tests are underway for 10 mRNA therapies, and with another 11 preclinical programs disclosed, Moderna shows no hesitation in exploring mRNA’s versatility. CEO Bancel has often said that Moderna’s total number of preclinical programs exceeds 100. “Our problem is trying to figure out what things to develop further,” CSO Moore explains. “We have an embarrassment of riches.”

Such bravado is one reason the company continues to garner scrutiny. But backing by pharma giants has helped legitimize Moderna and, more broadly, the field. “I know how Merck’s internal engine works. It is very science driven,” says Yusuf Erkul, a former cancer scientist at Merck & Co. “There is no way that Moderna would have got that funding without significant data to back it up.” After learning about the field, Erkul started his own mRNA therapy start-up, Kernal Biologics, in 2016, focused on cancer therapies.

Many scientists, including Nobel Prize winner Sharp, used to think mRNA therapy would be too technically difficult to make a reality. “They’ve totally convinced me it is possible to do,” he says of Moderna. Now it’s a matter of proving it works in humans and without side effects or complications that would encumber its practicality, Sharp adds. “That’s the litmus test.”

In the meantime, Moderna remains confident of its progress. “We already have things working,” Moore says. “There are no challenges that are limiting us in any way of getting stuff into the clinic.”

Moore is often asked how she feels about her jump from academia to industry. She doesn’t mince words about her decision. “It was a once-in-a-lifetime opportunity to use everything I’ve done in my career to develop an entirely new therapeutic modality that I think has the potential to completely disrupt the drug development and biologics space,” Moore says. “So, it is not industry. It is Moderna.”

CORRECTION

This story was updated on Sept. 5, 2018, to reflect the fact that BioNTech has made a drug development deal with Sanofi rather than Sanofi Pasteur, a Sanofi subsidiary.

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Comments

Dr. Paul C. Li (September 8, 2018 5:36 AM)

The uncertainty principle appears not limited to Quantum chemistry. It is every where in the molecular therapeutics. Retrospective view and perspective viewing in science and technology to prove better chemistry is made for better life, and life itself is chemistry. That keep on doing our best keeps everything alive.

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serafettin gunes (September 8, 2018 5:00 PM)

This is a great article for people like me who is relatively new to bio tech industry and that wants to learn about different therapy approaches. I am especially amazed by RNA technologies . Thank you for your efforts. I also want to thank much more and extend my sincere gratitude to all the true and dedicated scientist who work hard to make such scientific breakthroughs and make it available for patients who are suffering from horrible diseases ( or other discoveries that makes life better on earth )